The invention forms an epitaxial silicon-containing layer on a silicon germanium, patterned strained silicon, or patterned thin silicon-on-insulator surface and avoids creating a rough surface upon which the epitaxial silicon-containing layer is grown. In order to avoid creating the rough surface, the invention first performs a hydrofluoric acid etching process on the silicon germanium, patterned strained silicon, or patterned thin silicon-on-insulator surface. This etching process removes most of oxide from the surface, and leaves only a sub-monolayer of oxygen (typically 1×1013-1×1015/cm2 of oxygen) at the silicon germanium, patterned strained silicon, or patterned thin silicon-on-insulator surface. The invention then performs a hydrogen pre-bake process in a chlorine containing environment which heats the silicon germanium, strained silicon, or thin silicon-on-insulator surface sufficiently to remove the remaining oxygen from the surface. By introducing a small amount of chlorine containing gases, the heating processes avoid changing the roughness of the silicon germanium, patterned strained silicon, or patterned thin silicon-on-insulator surface. Then the process of epitaxially growing the epitaxial silicon-containing layer on the silicon germanium, patterned strained silicon, or patterned silicon-on-insulator surface is performed.